Structure of PDB 3dll Chain K Binding Site BS01

Receptor Information

>3dll Chain K (length=113) Species: 1299 (Deinococcus radiodurans)

HGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLI
TTAKGGDLHSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGT
RRGDGVTMALIEL

Ligand information

>3dll Chain X (length=2686)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaauc
aagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguagg
cgaacgagaggucguuguucgugaaacgaugacugaauccgcgcggacca
ccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugag
ggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccg
uggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauu
gaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaa
cggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucggg
cuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccgug
acagggggcggaggaccgaaccggugccugcugaaacagucucggaugag
uuguguuuaggagugaaaagcuaaccgaaccuggagauagcuaguucucc
ccgaaauguauugagguacagccucggauguugaccauguccuguagagc
acucacaaggcuaaaaccuuaugaaacuccgaaggggcacgcguuuaguc
cgggagugaggcugcgagagcuaacuuccguagccgagagggaaacaacc
cagaccaucagcuaaggucccuaaaugaucgcucagugguuaaggaugug
ucgucgcauagacagccaggagguuggcuuagaagcagccacccuucaaa
gagugcguaauagcucacuggucgagugacgaugcgccgaaaaugaucgg
ggcucaagugaucuaccgaagcuauggauucaacucgcgaagcgaguugu
cugguaggggagcguucaguccgcggagaagccauaccggaaggaguggu
ggagccgacugaagugcggaugccggcaugaguaacgauaaaagaaguga
gaaucuucuucgccguaaggacaaggguuccuggggaagggucguccgcc
cagggaaagucgggaccuaaggugaggccgaacggcgcagccgauggaca
gcaggucaagauuccugcaccgaucauguggagugauggagggacgcauu
acgcuauccaaugccaagcuauggcuaugcugguugguacgcucaagggc
gaucgggucagaaaaucuaccggucacaugccucagacguaucgggagcu
uccucggaagcgaaguuggaaacgcgacggugccaagaaaagcuucuaaa
cguugaaacaugauugcccguaccgcaaaccgacacagguguccgagugu
caaugcacuaaggcgcgcgagagaacccucguuaaggaacuuugcaaucu
caccccguaacuucggaagaagggguccccacgcuucgcguggggcgcag
ugaauaggcccaggcgacuguuuaccaaaaucacagcacucugccaacac
gaacaguggacguauagggugugacgccugcccggugccggaaggucaag
uggagcggugcaagcugcgaaaugaagccccggugaacggcuaagguagc
gaaauuccuugucggguaaguuccgaccugcacgaaaggcguaacgaucu
gggcgcugucucaacgagggacucggugaaauugaauuggcuguaaagau
gcggccuacccguagcaggacgaaaagaccccguggagcuuuacuauagu
cuggcauugggauucggguuucuagaaacuuggauuucuaaccugaaaaa
ucacuuucggggaccgugcuuggcggguaguuugacuggggcggucgccu
cccaaaauguaacggaggcgcccaaaggucaccucaagacgguuggaaau
cgucuguagagcgcaaagguagaagguggcuugacugcgagacugacacg
ucgagcagggaggaaacucgggcuuagugaaccggugguaccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagaguccauaucggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgcuacgggcgcaggagaauugaggggaguugcuccuaguacgaga
ggaccggagugaacggaccgcuggucucccugcugucguaccaacggcac
augcaggguagcuauguccggaacggauaaccgcugaaagcaucuaagcg
ggaagccagccccaagaugaguucucccacuguuuaucagguaagacucc
cggaagaccaccggguuaagaggccaggcgugcacgcauagcaauguguu
cagcggacuggugcucaucagucgaggucuugacca

<<<<<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<....
..<<<<<<.[...((.>>>.....<<<<<<...<<.))...]..>>....
..>>>>>>...>>>....<<<....>>><<<<<....>>>>><<<<....
>>>>>>...<<<<<<.....<<....>>......>>>>>.>.........
<<....>>...<<<<......<<.....>>.....>>>>...<<<...<<
..<<<...<<<<<......>>>>>((......<<<.....))>>>...>>
>....>>..<<<<<<<<<.......>>>>>>>>>......<<<<<..(((
(>>>>>..>>>......>>.>>>>>>.>>..............<<....>
>....>>.........<<<<....>>>>..................>>>>
>>>>>>>.......<<<<<<<<<<.......>>>>>>>>>>...<.<...
.....>.>.<<<<<<...<<<<.<<<<<<<<<<..<<<...<<<....>>
>...>>>...<<....>>...<........>.........>>>>>>>>>>
>>>>.<<.<...<<<<<<.....<<<<<<<<<..<<<.....<<<<<...
...>>>>>......>>>...<<<<.<.<<........>>.>>>>>....>
>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<
<<....<<<<<....>>>>><<<<<<<<<...<<<<.<<<<<<...<<<.
..<<<.<<<<......>>>>.>>>..>>.>...>>>>>>.>.>>>..>>>
>>>>.>>..<<<<<<<.<<......>>.>>>>>>>....<<<......>>
>...<<<<.<<<...<<<(((.....<<<<<<...........<<..<<<
<<<<<<........<<<<<.<<<..<<<<.......>>>>..>>>.....
....<<......>>...>>>>>....>>>>>>>>>.>>..........))
)......>>>>>>.>>>...>>>>>>>...<<<<<<<<...>>>>>>>>.
......>>>>>><.<<<<<<<.<<......<<<<<.<<....>>.>>>>>
...>>.>>>>>>>..>.....>>>>>><......<<.....<<<<<<...
....>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>
>>>>....((<<<<.<<...<<<...<<<<..>>>>...>>>...>>...
<<<<<........>>>>>))<<<<<<<<<...<<...<<<<....<<<<.
.<<<..<<<<<.<<<<.<<...[[....>>>>>><<<<<<<.<<..<<<<
<<<<<<...<<.....>>.>>>>>>....>>>>..>>>>>>>>>...<<<
<<....>>>>>....>>>>>...>>>...>>>>.........>>>>...>
>......>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<<
....>>>>>..>>>>..<<<<....<<<<<<<<.<<.........<....
.<<<<<...............>>>>><<<<<<<<...>>>>>>>>.....
.......<<<<<<<<<..<<...........>>..<<<<<<<.....<<<
.....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<
<...<<<<<....>>>>>...>>...>>>>>>>>..>>>>>.......<.
..........<<<<<.......>>>>>.....>....>>>>>..>>.>>>
>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<.......
.>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.<<
<.<<<<<.<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>...<<<.<<...
.....>>.>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<
<<...........>>>>>>..<<...<<<<<<<...<<<<<<.......>
>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<......>
>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<<..))))..
>>>>>>>>>.............>>>>..>>>>>>.......<<<<.<.<<
<<<<...<<.......>>...>>>>>>...>>>>.>.......<<<<<..
<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>.
....>>>>>......>>>.>>....<<<<<<<....>>>.>>>>......
..>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<..........
.....>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<.]].>>>>>>.
..>>>>>...>>>>.>>>>>....<<....<<<<<...........>>>>
>....>>..>>>>.......>>>>>>>..<<<.....>>>....<<<<<<
<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>.
..>>>..>>>>>.>>>...>>>>....>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dll The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): H3 K5 A6 G7 R8 L10 R12 S14 R22 E31 I34 T36 T39 K40 K42 Q50 T53 L60 H61 R63 R64 Q68 H71 K73 R90 P91 G92 G93 T95 R96 R99 R103 G105 D106 G107 V108
• Binding residue (residue number reindexed from 1): H1 K3 A4 G5 R6 L8 R10 S12 R20 E29 I32 T34 T37 K38 K40 Q48 T51 L58 H59 R61 R62 Q66 H69 K71 R88 P89 G90 G91 T93 R94 R97 R101 G103 D104 G105 V106

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3dll, PDBe:3dll, PDBj:3dll
• PDBsum: 3dll
• PubMed: 18757750
• UniProt: Q9RSJ5|RL17_DEIRA Large ribosomal subunit protein bL17 (Gene Name=rplQ)